Ben Kuznets-Speck
@biophysben.bsky.social
Biophysicist working at the edge of single cell biology, machine learning, and statistical-mechanics. Postdoc in Yogesh Goyal's lab at Northwestern; PhD in biophysics, UC Berkeley; BS in math and physics, CWRU.
Reposted by Ben Kuznets-Speck
NEW PREPRINT led by stellar postdoc
@biophysben.bsky.social We turn diffusion models into inference machines. Score function→exact likelihoods, uncertainty estimate & interpretablity. Diffusion models generate. But classify? Untapped—until now @chanzuckerberg.bsky.social shorturl.at/s32uX
@biophysben.bsky.social We turn diffusion models into inference machines. Score function→exact likelihoods, uncertainty estimate & interpretablity. Diffusion models generate. But classify? Untapped—until now @chanzuckerberg.bsky.social shorturl.at/s32uX
December 2, 2025 at 6:03 PM
NEW PREPRINT led by stellar postdoc
@biophysben.bsky.social We turn diffusion models into inference machines. Score function→exact likelihoods, uncertainty estimate & interpretablity. Diffusion models generate. But classify? Untapped—until now @chanzuckerberg.bsky.social shorturl.at/s32uX
@biophysben.bsky.social We turn diffusion models into inference machines. Score function→exact likelihoods, uncertainty estimate & interpretablity. Diffusion models generate. But classify? Untapped—until now @chanzuckerberg.bsky.social shorturl.at/s32uX
Today we’re excited to share Keeping SCORE, a framework that turns any diffusion model into a thermodynamic inference machine.
Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...
Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...
December 2, 2025 at 1:32 AM
Today we’re excited to share Keeping SCORE, a framework that turns any diffusion model into a thermodynamic inference machine.
Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...
Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...
Reposted by Ben Kuznets-Speck
Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.
November 18, 2025 at 2:19 AM
Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.
Reposted by Ben Kuznets-Speck
excited to announce that this January we are relocating to Yale to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI): @yalecsei.bsky.social
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
SPE - join us
Postdoctoral position:
In January 2026, we are relocating to Yale university to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI).
We are looking for talented postd...
sites.google.com
October 27, 2025 at 8:47 PM
excited to announce that this January we are relocating to Yale to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI): @yalecsei.bsky.social
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
Reposted by Ben Kuznets-Speck
Babies who are threat to DHS = 0
DHS teargas grenades thrown at babies = More than 0
(Before anyone blames adults for bringing baby there, video shows woman pull baby from her obstructed car to escape area. No indication she was there for a protest.)
DHS teargas grenades thrown at babies = More than 0
(Before anyone blames adults for bringing baby there, video shows woman pull baby from her obstructed car to escape area. No indication she was there for a protest.)
Yeah, that is a tear gas canister being fired toward the retreating couple holding the baby
October 15, 2025 at 3:24 AM
Babies who are threat to DHS = 0
DHS teargas grenades thrown at babies = More than 0
(Before anyone blames adults for bringing baby there, video shows woman pull baby from her obstructed car to escape area. No indication she was there for a protest.)
DHS teargas grenades thrown at babies = More than 0
(Before anyone blames adults for bringing baby there, video shows woman pull baby from her obstructed car to escape area. No indication she was there for a protest.)
Reposted by Ben Kuznets-Speck
September 29, 2025 at 5:55 PM
Reposted by Ben Kuznets-Speck
Trying to log into Eduroam
September 29, 2025 at 12:56 PM
Trying to log into Eduroam
Reposted by Ben Kuznets-Speck
There is no world in which masked and armed agents of the state running down delivery drivers makes us safer. That our information environment and political leaders have convinced people otherwise is a massive failure.
ICE Nazis in Chicago tried to kidnap a food delivery worker but my man was too fast for those slow bastards
September 29, 2025 at 1:39 AM
There is no world in which masked and armed agents of the state running down delivery drivers makes us safer. That our information environment and political leaders have convinced people otherwise is a massive failure.
Reposted by Ben Kuznets-Speck
I finished my estimate on required compute to make an atomic-resolution virtual cell: 10^38 FLOPs to simulate a human cell for 1 day. We should be able to do this simulation in 2074 using 200 TW of power. 1/3
September 26, 2025 at 3:19 PM
I finished my estimate on required compute to make an atomic-resolution virtual cell: 10^38 FLOPs to simulate a human cell for 1 day. We should be able to do this simulation in 2074 using 200 TW of power. 1/3
Excited to share my new work on using AI and measured transcriptional responses to gene perturbations (knockdowns for example) to predict which sets of genes cause/mitigate complex disease phenotypes like cancer metastasis, IBD, or asthma, out now in PNAS! www.pnas.org/doi/full/10....
September 23, 2025 at 1:59 PM
Excited to share my new work on using AI and measured transcriptional responses to gene perturbations (knockdowns for example) to predict which sets of genes cause/mitigate complex disease phenotypes like cancer metastasis, IBD, or asthma, out now in PNAS! www.pnas.org/doi/full/10....
Reposted by Ben Kuznets-Speck
A whistleblower complaint says that the personal data of over 300 million Americans was copied to a private cloud account to allow access by members of the Department of Government Efficiency team.
Whistleblower says Trump officials copied millions of Social Security numbers
A whistleblower complaint says that the personal data of over 300 million Americans was copied to a private cloud account to allow access by members of the Department of Government Efficiency team.
n.pr
August 26, 2025 at 7:57 PM
A whistleblower complaint says that the personal data of over 300 million Americans was copied to a private cloud account to allow access by members of the Department of Government Efficiency team.
Reposted by Ben Kuznets-Speck
This is not just HHMI. All Chan Zuckerberg Initiative funding calls are CLOSED. The Gates Foundation has no Grand Challenges funding opportunities. I've never seen anything like this. Private foundations have just decided to stop supporting biomedical research.
August 9, 2025 at 4:50 PM
This is not just HHMI. All Chan Zuckerberg Initiative funding calls are CLOSED. The Gates Foundation has no Grand Challenges funding opportunities. I've never seen anything like this. Private foundations have just decided to stop supporting biomedical research.
Reposted by Ben Kuznets-Speck
A reminder that the mRNA vaccine technology saved millions of lives during the Covid pandemic and received the 2023 Nobel Prize for Medicine
August 10, 2025 at 12:26 AM
A reminder that the mRNA vaccine technology saved millions of lives during the Covid pandemic and received the 2023 Nobel Prize for Medicine
Reposted by Ben Kuznets-Speck
I don’t have a problem with someone evaluating my science abilities if I have the ability to examine theirs.
Let’s do televised qualifying exams for all the political appointees who will be evaluating science grants and proposals. Let’s start with directors of institutes and cabinet secretaries.
Let’s do televised qualifying exams for all the political appointees who will be evaluating science grants and proposals. Let’s start with directors of institutes and cabinet secretaries.
August 7, 2025 at 11:00 PM
I don’t have a problem with someone evaluating my science abilities if I have the ability to examine theirs.
Let’s do televised qualifying exams for all the political appointees who will be evaluating science grants and proposals. Let’s start with directors of institutes and cabinet secretaries.
Let’s do televised qualifying exams for all the political appointees who will be evaluating science grants and proposals. Let’s start with directors of institutes and cabinet secretaries.
Reposted by Ben Kuznets-Speck
How challenging is the prediction of transcriptional responses to CRISPR gene perturbations ?
A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations.
The model is intuitive & grounded in a simple approximation.
1/2
A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations.
The model is intuitive & grounded in a simple approximation.
1/2
July 24, 2025 at 11:00 AM
How challenging is the prediction of transcriptional responses to CRISPR gene perturbations ?
A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations.
The model is intuitive & grounded in a simple approximation.
1/2
A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations.
The model is intuitive & grounded in a simple approximation.
1/2
Reposted by Ben Kuznets-Speck
Paper in Nature 150 years ago. Beats reading any single-cell experiment…
July 17, 2025 at 3:10 PM
Paper in Nature 150 years ago. Beats reading any single-cell experiment…
Reposted by Ben Kuznets-Speck
"Grant cancellations and budget reductions at the National Institutes of Health have put millions of dollars in research for promising new cancer treatments, tuberculosis therapies, and much more in jeopardy."
www.scientificamerican.com/article/atta...
www.scientificamerican.com/article/atta...
Apathy Over Attacks on Higher Education Needs to Change
If Americans don’t fight back against efforts to dismantle higher education, the U.S. will lose lifesaving medical research, innovation that spurs our economy and the ability to freely study science a...
www.scientificamerican.com
July 10, 2025 at 10:01 PM
"Grant cancellations and budget reductions at the National Institutes of Health have put millions of dollars in research for promising new cancer treatments, tuberculosis therapies, and much more in jeopardy."
www.scientificamerican.com/article/atta...
www.scientificamerican.com/article/atta...
Reposted by Ben Kuznets-Speck
Under Trump, NOAA ran the most recent competition for their highly prestigious postdoc program in climate and global change — but funded no one, wasting huge amounts of applicant and reviewer time.
It gets a lot worse. Now current postdocs in the program are going unpaid.
It gets a lot worse. Now current postdocs in the program are going unpaid.
Recipients of a U.S. Climate Science Fellowship Are Put on Unpaid Leave
www.nytimes.com
July 9, 2025 at 7:22 PM
Under Trump, NOAA ran the most recent competition for their highly prestigious postdoc program in climate and global change — but funded no one, wasting huge amounts of applicant and reviewer time.
It gets a lot worse. Now current postdocs in the program are going unpaid.
It gets a lot worse. Now current postdocs in the program are going unpaid.
Reposted by Ben Kuznets-Speck
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
July 7, 2025 at 5:27 PM
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
www.cell.com/cell-systems...
Reposted by Ben Kuznets-Speck
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw
July 6, 2025 at 10:11 PM
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw